From 636e27b006d54dc50c235f3d0e54e6d47c56a08d Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Fri, 26 Mar 2021 01:13:58 -0400
Subject: [PATCH] Fix SA Mutable (see details)

The ``sqlalchemy.ext.mutable`` extension now tracks the "parents"
collection using the :class:`.InstanceState` associated with objects,
rather than the object itself. (see Ref)

This commit updates our implementation of these methods
(required for SQLAlchemy>=1.4.2)

Ref:
https://github.com/sqlalchemy/sqlalchemy/discussions/6018
https://github.com/sqlalchemy/sqlalchemy/commit/1031fc6f781a3a6088467791e837f23a4b338aef#
---
 lib/galaxy/model/custom_types.py   | 9 +++++----
 lib/galaxy/model/database_utils.py | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index ca2062504e3e..0eb9618b1283 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -10,6 +10,7 @@
 import numpy
 import sqlalchemy
 from sqlalchemy.ext.mutable import Mutable
+from sqlalchemy.inspection import inspect
 from sqlalchemy.types import (
     CHAR,
     LargeBinary,
@@ -152,15 +153,15 @@ def load(state, *args):
                 val = cls.coerce(key, val)
                 state.dict[key] = val
             if isinstance(val, cls):
-                val._parents[state.obj()] = key
+                val._parents[state] = key
 
         def set(target, value, oldvalue, initiator):
             if not isinstance(value, cls):
                 value = cls.coerce(key, value)
             if isinstance(value, cls):
-                value._parents[target.obj()] = key
+                value._parents[target] = key
             if isinstance(oldvalue, cls):
-                oldvalue._parents.pop(target.obj(), None)
+                oldvalue._parents.pop(inspect(target), None)
             return value
 
         def pickle(state, state_dict):
@@ -173,7 +174,7 @@ def pickle(state, state_dict):
         def unpickle(state, state_dict):
             if 'ext.mutable.values' in state_dict:
                 for val in state_dict['ext.mutable.values']:
-                    val._parents[state.obj()] = key
+                    val._parents[state] = key
 
         sqlalchemy.event.listen(parent_cls, 'load', load, raw=True, propagate=True)
         sqlalchemy.event.listen(parent_cls, 'refresh', load, raw=True, propagate=True)
diff --git a/lib/galaxy/model/database_utils.py b/lib/galaxy/model/database_utils.py
index c9193357e0aa..4baf6d6da4a0 100644
--- a/lib/galaxy/model/database_utils.py
+++ b/lib/galaxy/model/database_utils.py
@@ -60,7 +60,7 @@ class PosgresDatabaseManager(DatabaseManager):
 
     def _handle_no_database(self):
         self.database = self.url.database  # use database from db_url
-        self.url = self.url.set(database = 'postgres')
+        self.url = self.url.set(database='postgres')
 
     def exists(self):
         with sqlalchemy_engine(self.url) as engine: